I think this was alluded to in this post, but I didn't see (and I haven't been able to figure out a way around) my exact issue. I'm not using Meta Box for the registration portion of what I'm working on, but still am using the user (profile & meta) extensions for the user profile itself. The shortcode form works great, however the $config ids include all username, password, etc. so every time I've been updating profiles during my validation testing for my application, it throws up a warning sign.
The workaround is to simply display:none that banner, and everything updates as it should. But I try to avoid kludgy workarounds if I can, so if you know which filter or action can remove those $configs (or at least remove the warning banner), that would be great.